Abstract: The work discussed in this talk falls into the emerging area of
Population Genomics. I will first introduce that area and then
talk about specific problems and results involved in the
inference of recombination from population data.

A phylogenetic network (or Ancestral Recombination Graph) is a
generalization of a tree, allowing structural properties that are not
tree-like. With the growth of genomic and population data (coming for example
from the HAPMAP project) much of
which does not fit ideal tree models, and the increasing appreciation
of the genomic role of such phenomena as recombination (crossing-over
and gene-conversion), recurrent and back mutation, horizontal gene
transfer, and mobile genetic elements, there is greater need to
understand the algorithmics and combinatorics of phylogenetic
networks.

In this talk I will survey a range of our recent results on
phylogenetic networks with recombination and show applications of
these results to several issues in Population Genomics:
Association Mapping; Finding Recombination Hotspots in
genotype sequences; Imputing the values of missing haplotype data;
Determining the extent of recombination in the evolution of LPL
sequences; Distinguishing the role of crossing-over from
gene-conversion in Arabidopsis; Characterizing some aspects of the
haplotypes produced by the program PHASE; Studying the effect of
using genotype data in place of haplotype data, etc.

Various parts of this work are joint work with Satish Eddhu, Chuck
Langley, Dean Hickerson, Yun Song, Yufeng Wu, V. Bansal, V. Bafna
and Zhihong Ding. Papers and associated software can be accesses at
http://wwwcsif.cs.ucdavis.edu/~gusfield/

Short Bio: Professor Gusfield's background is in Combinatorial Optimization, and
various applications of Combinatorial Optimization. He has worked
extensively on problems of network flow, matroid optimization,
statistical data security, stable marriage and matching, string
algorithms and sequence analysis, phylogenetic tree inference,
haplotype inference, and inference of phylogenetic networks with
homoplasy and recombination. He received his Ph.D. in 1980 from UC
Berkeley, working with Richard Karp, and was an Assistant Professor at
Yale University from 1980 to 1986.

Professor Gusfield moved to UC Davis in July 1986. Since then, he has
mostly addressed problems in Computational Biology and Bioinformatics.
He first addressed questions about building evolutionary trees, and
then problems in molecular sequence analysis. He presently focuses
mostly on optimization problems related to population genetics and
population-scale genomics. Two particular problems are haplotype
inference and inferences about historical recombination. His main
support for work on computational biology and bioinformatics came
initially from the Department of Energy Human Genome Project through
the Lawrence Berkeley Labs Human Genome Center, then directly from DOE,
Human Genome Project, but since then, his work in computational biology
has been funded by the NSF. His book, ``Algorithms on Strings, Trees
and Sequences: Computer Science and Computational Biology" has helped
to define the intersection of computer science and bioinformatics. It
has been translated into Russian, and a South Asian edition has recently been
published. Professor Gusfield serves on the editorial board of the
Journal of Computational Biology, and is the founding Editor-in-Chief
of The IEEE/ACM Transactions on Computational Biology and
Bioinformatics. The journal was presented the ``honorable mention" for
Best New Journal in 2004 by the American Association of Publishers.
Other notable service to the Computational Biology community consists
of serving as Program Chair for the 2004 RECOMB conference.

At UCD, Professor Gusfield was chair of the Computer Science
Department for four years, and wrote the bioinformatics section (one of
three) of the Genomics/Bioinformatics initiative proposal that resulted
in the creation of the UCD Genomics Center (which has hired 17 new
faculty), and continues to serve on its internal Steering committee. He
is currently co-chair of the UCD campus initiative on ``Computational
Characterization and Exploitation of Biological Networks" (see
cnb.ucdavis.edu), which will hire seven new faculty in this area over the
next three years.